Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes

Background Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus. Results We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots—mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT. Conclusions Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-024-01924-y.

The tree is condensed under a 50% majority rule.

Fig. S2 .
Fig. S2.Draft mitogenome map of Gnetum ula.Grey bars represent 21 linear scaffolds.Loci are color-coded depending on their origins.Light-blue histograms denote DNA read depths in log scale.SC, scaffold.

Fig. S3 .
Fig. S3.A ML tree inferred from ccmB using ferns as the outgroup.Subtrees within left boxes indicate the relative placements of foreign and native ccmB genes in Gnetum with bootstrap values under a 50% majority rule.

Fig. S4 .
Fig. S4.A ML tree inferred from ccmFc using ferns as the outgroup.Subtrees within left boxes indicate the relative placements of foreign and native ccmFc genes in Gnetum with bootstrap values under a 50% majority rule.

Fig. S5 .
Fig. S5.A ML tree inferred from ccmFn using ferns as the outgroup.Subtrees within left boxes indicate the relative placements of foreign and native ccmFn genes in Gnetum with bootstrap values under a 50% majority rule.

Fig. S6 .
Fig. S6.A ML tree inferred from matR using ferns as the outgroup.Subtrees within left boxes indicate the relative placements of foreign and native matR genes in Gnetum with bootstrap values under a 50% majority rule.

Fig. S7 .
Fig. S7.A ML tree inferred from nad1 exons 2-3 using ferns as the outgroup.Subtrees within left boxes indicate the relative placements of foreign and native nad1 exons 2-3 loci in Gnetum with bootstrap values under a 50% majority rule.

Fig. S8 .
Fig. S8.A ML tree inferred from nad1 exons 4-5 using ferns as the outgroup.Subtrees within left boxes indicate the relative placements of foreign and native nad1 exons 4-5 loci in Gnetum with bootstrap values under a 50% majority rule.

Fig. S9 .
Fig. S9.A ML tree inferred from nad5 exons 4-5 using ferns as the outgroup.Subtrees within left boxes indicate the relative placements of foreign and native nad5 exons 4-5 loci in Gnetum with bootstrap values under a 50% majority rule.

Fig. S10 .
Fig. S10.A ML tree inferred from rps1 using ferns as the outgroup.The subtree indicates the relative placement of foreign rps1 genes in Gnetum with bootstrap values under a 50% majority rule.The native rps1 has been lost from Gnetum and thus was not included in this tree.

Fig
Fig. S11.A ML tree inferred from plastid (native) and mitochondrial plastid-derived (foreign) rps7 using ferns as the outgroup.Note that Gnetum's plastid loci are separated from their mitochondrial homologs, suggesting that the latter are HGT loci rather than MTPTs.Subtrees detail the relative placements of foreign and native rps7 genes in Gnetum with bootstrap values under a 50% majority rule.

Fig. S12 .
Fig. S12.A ML tree inferred from plastid (native) and mitochondrial plastid-derived (foreign) ndhB using ferns as the outgroup.The two remote clades in Gnetum suggest that two independent HGT events have taken place in the Asia clades I and II, respectively.Subtrees detail the relative placements of foreign ndhB loci in Gnetum with bootstrap values under a 50% majority rule.The plastid ndhB has been lost from Gnetum and thus was not included in this tree.

Fig. S13 .
Fig. S13.A ML tree inferred from rps13 using ferns as the outgroup.The subtree details the relative placements of foreign rps13 genes in Gnetum with bootstrap values under a 50% majority rule.The native rps13 has been lost from Gnetum and thus was not included in this tree.

Fig. S14 .
Fig. S14.A ML tree inferred from cox2 using ferns as the outgroup.Subtrees show the relative placements of foreign and native cox2 gene in Gnetum with bootstrap values under a 50% majority rule.

Fig. S15 .
Fig. S15.A ML tree inferred from nad6 using ferns as the outgroup.Subtrees show the relative placements of foreign and native nad6 genes in Gnetum with bootstrap values under a 50% majority rule.

Fig. S16 .
Fig. S16.A ML tree inferred from plastid, native MTPT, and foreign MTPT copies of psaA using ferns as the outgroup.Subtrees detail the relative placements of these three psaA copies in Gnetum with bootstrap values under a 50% majority rule.

Fig. S17 .
Fig. S17.A ML tree inferred from plastid, native MTPT, and foreign MTPT copies of psaB using ferns as the outgroup.Subtrees detail the relative placements of these three psaB copies in Gnetum with bootstrap values under a 50% majority rule.

Fig. S18 .
Fig. S18.A ML tree inferred from rpl10 using ferns as the outgroup.Subtrees detail the relative placements of foreign and native rpl10 genes in Gnetum with bootstrap values under a 50% majority rule.The native rpl10 has been lost from all sampled Gnetum species within the Asia clade II, except for G. ula whose rpl10 is retained but pseudogenized.

Fig. S19 .
Fig. S19.A ML tree inferred from rps3 using ferns as the outgroup.Subtrees show the relative placements of foreign and native rps3 genes in Gnetum with bootstrap values under a 50% majority rule.

Fig. S20 .
Fig. S20.A ML tree inferred from rps4 using ferns as the outgroup.Subtrees detail the relative placements of foreign and native rps4 genes in Gnetum with bootstrap values under a 50% majority rule.

Fig. S21 .
Fig. S21.A ML tree inferred from atp4 using ferns as the outgroup.Subtrees indicate the relative placements of foreign and native atp4 in Gnetum with bootstrap valuesunder a 50% majority rule.In Gnetum, the close relative to foreign atp4 is uncertain, so that the possible donor of this foreign gene is designated as questionable ("?") in Figure 2.

Fig. S22 .
Fig. S22.Comparison of mitochondrial RNA expression level between foreign and native genes in G. parvifolium and G. ula.

Fig. S23 .
Fig. S23.A ML tree inferred from the flanking region of the 3' end of the Coptosapelta-derived ndhB exon1 & intron locus and its mitochondrial homologies.

Fig. S24 .
Fig. S24.A ML tree inferred from the flanking region of the 3'end of the Malpighialesderived psaB locus and Its mitochondrial homologies.The tree is condensed under a 50% majority rule.